-transparent.png){kind=logo}
We describe and evaluate the image-processing and analysis techniques we have developed for the quantitative analysis of comparative genomic hybridization (CGH; Science 258:818, 1992). In a typical CGH application, two genomic DNA samples are simultaneously hybridized to metaphase chromosomes and detected with different fluorochromes. The primary data in CGH are contained in the intensity ratios of the fluorochromes as a function of position on the chromosomes, which reflect variation in DNA copy number ratio between the two DNA samples. Analysis involves chromosome segmentation, intensity normalization, background corrections, and calculation of the fluorescence intensity profiles and the ratio profile along the chromosome's length. Profiles from several copies of the same chromosome in different metaphases are averaged to reduce the noise. Confidence intervals are calculated and displayed for the mean profiles. The techniques were evaluated by examining the variability found in comparisons of two normal genomic DNAs, where the ratio was expected to be constant, and by measuring the ratios obtained for cell lines with cytogenetically documented copy number changes involving several chromosomal segments. The limits of sensitivity of CGH analysis were investigated by simulation. Guidelines for the interpretation of CGH data and indications of areas for future development of the analytical techniques are also presented.
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
January 1995,
Cytometry,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
December 2001,
Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
January 2002,
Methods in molecular medicine,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
February 2000,
Genes, chromosomes & cancer,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
January 1995,
Cytometry,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
January 2003,
Journal of neurosurgery,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
December 1997,
Analytical and quantitative cytology and histology,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
July 2002,
The Journal of clinical endocrinology and metabolism,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
January 1997,
Cytogenetics and cell genetics,
J Piper, and
D Rutovitz, and
D Sudar, and
A Kallioniemi, and
O P Kallioniemi, and
F M Waldman, and
J W Gray, and
D Pinkel
January 2006,
International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics,
